Questions tagged [pymol]
a molecular visualization system created by Warren Lyford DeLano. This tag can be used in questions related to the use and the visualizations produced using this software.
10 questions
0
votes
2
answers
86
views
How to select residues in a selection for protein mutagenesis in PyMOL?
Currently I am creating a selection that has residues 5 angstroms away from a ligand for alanine point mutations at each highlighted residue. Currently, the code is creating the specific selections I ...
0
votes
1
answer
477
views
How to color based on b-factor for all the frames in one object in Pymol?
I load a protein.pdb file into Pymol. This file has multiple frames (or states), and with different b-factor values at different ...
- 253
1
vote
1
answer
77
views
Examining antibody - target interactions in PyMOL
I'm a student currently looking at antibody responses against a viral target protein of interest.
I have my own, annotated PyMOL session of my protein and I also have .pdbs of crystallised antibody ...
- 19
3
votes
0
answers
307
views
Automating figure-making with PyMOL [closed]
What I want to do
I have a list of almost 200 PDB entries that I need to visually inspect. Luckily, the thumbnail image displayed on the PDB website (examples with RCSB or PDBe for a well-known ...
- 715
2
votes
1
answer
1k
views
Can pymol show cartoon (secondary structure) for a pdb of multiple frames?
I am using pymol to visualise the secondary structure of protein using its cartoon representation. The ...
- 253
3
votes
1
answer
3k
views
How to perform a DNA structural alignment in pymol
How can I "fit" two DNA structures having different nucleotide sequences in PyMol?
I would like to use the structure of a DNA-binding protein in PDB (1h9t), which is bound to DNA in the PDB file, ...
- 41
3
votes
1
answer
3k
views
Generate full dimer from monomer with C2 symmetry?
I downloaded a PDB file of a dimer, but it only contains the monomer, and it says that the dimer can be obtained from C2 symmetry. For an example see here: http://www.rcsb.org/pdb/explore/explore.do?...
- 1,347
2
votes
1
answer
114
views
Is there a way to see what representations are currently displayed in PyMOL?
I am using PyMol to visualize .pdb protein structures.
I show/hide representation a lot, and sometimes I get confused with what representations are currently displayed. So I end up with doing a lot ...
- 185
2
votes
0
answers
597
views
Turn off multithreading in pymol [closed]
By default, pymol seems to grab the number of cores on the system for rendering. How can I force it to only use one core?
Motivation:
I have a large collection ...
- 211
15
votes
1
answer
2k
views
How do I get the current "camera position" in PyMol so I can reuse it in scripts?
I have a few protein models I want to take pictures of with various ligands bound. It would be nice if I could do it from the same "position", but the only way I can figure out to repeat the same ...
- 2,358